confused by bowtie2 alignment score

[capricy]

Hello, there,

I am using default mode for bowtie2 reporting and the manual has it "Bowtie 2 does not garantee that the alignment reported is the best possible in terms of alignment score"


The manual also has: It will eventually stop looking, ... or because it already knows all it needs to know to report an alignment

I am really confused by these sentences... Does it mean that other than the reported alignment, the one with better alignment score might be exist?

Thanks for any input!!

[tirohia]

Others may correct me if I'm wrong, but I've always understood that to be yes, there might exist an alignment with a better score. It finds the best alignment it can given the constraints on it - those being either

a) the number of seed extensions that fail and the number of reseed attempts (the -D and -R options in the manual right under the bit you're quoting)

or b) some other constraint, like if you have set -k 2 which asks bowtie2 to return 2 alignments. Once it's found 2 alignments, it knows all it needs to know to report and thus does so.

There has to be some constraints on the search, if there wasn't it could take a long, long time to finish.

Ben.